Microbiology Commons^™

Developing A Microdialysis Sampling-Based Biofilm/Macrophage Co-Culture Model, Alda Diaz Perez

Graduate Theses and Dissertations

The host immune system and bacterial cells are known to interact during the human lifetime. Bacteria secrete a wide variety of signaling molecules, known as quorum sensing (QSC) molecules, that modulate the host immune system. While immune-biofilm interactions involve this chemical signaling network, the mechanisms through which this occurs are not well understood. This work aimed to develop a new method that can be used not only in vitro settings but also in vivo. The microdialysis sampling technique has widely been used in in vitro and in vivo settings in humans, mice, and rats for the collection of neuropeptides, cytokines, …

College Of Natural Sciences Newsletter, May 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 5.

Page 1 Dean's Message
Page 2 - 3 Awards & Recognition
Page 4 Research Spotlight: Dr. Xiaoyang Zhang
Page 5 Upcoming Retirements
Page 6 - 7 Geography Alumni Social, Recent Media Coverage
Page 8 Open PRAIRIE Data
Page 9 - 11 Spring 2021 Dean's List and Academic Recognitions

Microbially-Mediated Carbonate Dissolution And Precipitation; Towards A Protocol For Ex-Situ, Cave-Analogue Cultivation Experiments, Vanessa E. Johnston, Andrea Martín-Pérez, Sara Skok, Janez Mulec

International Journal of Speleology

Subterranean calcite dissolution and precipitation are often considered as strictly geochemical processes. The active involvement of microbes in these processes is commonly underestimated in the literature due to general oligotrophic conditions in caves, except in particular cave conditions, such as sulfidic caves and moonmilk deposits, where the presence of microbes likely plays a key role in mineral deposition. Here, we study the possible involvement of microbes from Postojna Cave, Slovenia, in carbonate dissolution (litholysis) and precipitation (lithogenesis). Microbes were sampled from small pools below hydrologically diverse drip sites and incubated on polished limestone tablets at 10 and 20°C for 2 …

Human Ace2‑Functionalized Gold “Virus‑Trap” Nanostructures For Accurate Capture Of Sars‑Cov‑2 And Single‑Virus Sers Detection, Yong Yang, Yusi Peng, Chenglong Lin, Li Long, Jingying Hu, Jun He, Hui Zeng, Zhengren Huang, Zhi-Yuan Li, Masaki Tanemura, Jianlin Shi, John R. Lombardi, Xiaoying Luo

Publications and Research

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold “virus traps” nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106- fold virus enrichment originating from high-affinity of ACE2 with S protein as well as “virus-traps” composed of oblique gold nanoneedles, and 109- fold enhancement of Raman signals originating from multicomponent SERS effects. Furthermore, the identification standard of virus …

College Of Natural Sciences Newsletter, April 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 4

Page 1 Dean's Message
Page 2 & 3 Awards & Recognition
Page 4 Student Spotlight: Allsion Bjornstad
Page 5 Research Spotlight: Dr. Vondruska & Students
Page 6 Department Head Interviews
Page 7 Media Coverage of CNS
Page 8 Open PRAIRIE Data
Page 9 Student Club Spotlight: BMGSA
Page 10 Then & Now: Urban Geography

Taxonomic Annotation Of Near-Coral Seawater Microbiota In Kilifi, Kenya, Megan Ruoff

Independent Study Project (ISP) Collection

The general objective of this study was to analyze the microbiome of seawater above a coral reef in Kilifi, Kenya. Specific objectives included establishing a baseline microbiota profile, classifying the identified organisms at various taxonomic levels, and conjecturing about reef health from the presence or absence of bioindicator species including Vibrio bacteria. Sequenced 16S rRNA gene sequences from seawater samples at Kuruwitu Conservancy in Kilifi, Kenya were taxonomically classified by exact matching employing the Dada2 software package and the naïve Bayesian classifier method with 97% similarity cut off. The seawater microbiota contained mostly Proteobacteria (73.28%), followed by Bacteroidetes (14.08%) and …

Evaluating The Role Of The Stringent Response Mechanism In Clostridioides Difficile Survival And Pathogenesis, Astha Pokhrel

Chemistry & Biochemistry Theses & Dissertations

The human pathogen Clostridioides difficile is increasingly tolerant of multiple antibiotics and causes infections with a high rate of recurrence, creating an urgent need for new preventive and therapeutic strategies. The stringent response, a universal bacterial response to extracellular stresses, governs antibiotic survival and pathogenesis in diverse organisms but has not previously been characterized in C. difficile. This dissertation explores the ability of C. difficile to mount the stringent response. The bacteria encode a full-length, canonical bifunctional Rel/Spo Homolog or RSH enzyme. C. difficile RSH is incapable of utilizing GTP as a substrate but readily synthesizes putative 5’-pGpp-3’ alarmones. …

Microbiological Study In A Gneissic Cave From Sri Lanka, With Special Focus On Potential Antimicrobial Activities, Ethige Isuru P. Silva, Pathmakumara Jayasingha, Saman Senanayake, Anura Dandeniya, Dona Helani Munasinghe

International Journal of Speleology

The emergence of antibiotic resistance is a global health crisis, thus the search for novel antimicrobial compounds has become a continuous necessity. Underexplored and extreme environments, such as cave ecosystems, have been identified as a promising potential source for the discovery of novel microorganisms with novel antimicrobial compounds (AMC). This study presents the first cave microbiological investigation in Sri Lanka, with a special preference for bioprospecting of novel AMC. The cave sediment characterization demonstrated the presence of close to strong acidic conditions (pH 3.1 – 3.3) and thus indicates the possibility of isolating acidophilic microorganisms. Eight cave wall/ceiling fungal strains …

College Of Natural Sciences Newsletter, March 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2. Issue 3

Contents:

Page 1 Dean's Message
Page 2-3 Awards and Recognition
Page 4 Student Club Spotlight: MICROBIOLOGY CLUB
Page 5 Research Spotlight: Dr. Chakravarty
Page 6 Open PRAIRIE Data; Grants Awarded in CNS; Research Collquia
Page 7 A Busy Month in Review; Media Coverage of the College

3d Printing Of Human Microbiome Constituents To Understand Spatial Relationships And Shape Parameters In Bacteriology, Jacques Izard, Teklu Kuru Gerbaba, Shara R. P. Yumul

Department of Food Science and Technology: Faculty Publications

Effective laboratory and classroom demonstration of microbiome size and shape, diversity, and ecological relationships is hampered by a lack of high-resolution, easy-to-use, readily accessible physical or digital models for use in teaching. Three-dimensional (3D) representations are, overall, more effective in communicating visuospatial information, allowing for a better understanding of concepts not directly observable with the unaided eye. Published morphology descriptions and microscopy images were used as the basis for designing 3D digital models, scaled at 20,000×, using computer-aided design software (CAD) and generating printed models of bacteria on mass-market 3D printers. Sixteen models are presented, including rod-shaped, spiral, flask-like, vibroid, …

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …

Sustainable Bioproduction By Rhodopseudomonas Palustris Tie-1 Through Metabolic Engineering, Wei Bai

McKelvey School of Engineering Graduate Student Theses & Dissertations

The heavy reliance of the petroleum industry for raw material and the rising atmospheric CO2 caused by this reliance have driven the research and development of sustainable alternatives. Microbial production of chemicals, such as fuel and plastic, has been viewed as a feasible method. The wide selection of substrates by microbes enables them to produce chemicals using naturally abundant material or industrial waste, such as CO2, making the production sustainable. Compared to the model organisms such as Escherichia coli, Saccharomyces cerevisiae, many non-model organisms have a broader selection for carbon, electron, and nitrogen sources, making them great candidates for sustainable …

Characterization Of Microbial Populations In Landfill Leachate, Umut M. Bicim, Hanna Fulford, Lori A. Hoagland, Alejandro R. Sanchez, Amisha D. Shah, Inez Hua

Discovery Undergraduate Interdisciplinary Research Internship

In the United States, municipal solid waste (MSW) landfills remain a potential mining source of recoverable materials, including but not limited to critical, precious, and rare earth metals found in electronic waste. This is possible due to collectible leachate that filters through MSW landfills, carrying metals, nutrients of value, and microbes—some of which may hold key metal bioleaching properties—within. The purpose of this study is to begin analyzing leachate from MSW landfills in the American Midwest to understand the composition of microbial communities within these landfills. Landfill leachate samples sourced in northern Indiana, representing the landfill process during unique times …

Assaying Bacillus Amyloliquefaciens Isolates 1ba And 1d3 For Biosurfactant Production And Utilization Of Petroleum Hydrocarbons And Phenolic Acids, Pavan Kulkarni

Electronic Theses and Dissertations

Several Bacillus amyloliquefaciens isolates obtained from wheat residue have been studied as biological agents to control wheat diseases. Notable traits of isolates 1BA and 1D3 include growth with high salt (10% NaCl), at temperatures up to 50°C and over a wide pH range. BIOLOG Gen III plates were used to study and further characterize Bacillus amyloliquefaciens 1BA and 1D3. Both isolates showed tolerance to high salt concentration supporting previous studies. They also grew in the presence of lithium chloride, potassium tellurite, and sodium bromate. Both isolates grew at pH 5, with almost identical carbon source utilization fingerprints. However, D-serine, quinic …

College Of Natural Sciences 2021 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Welcome, Table of Contents
Page 3 Our Departments: Highlights From 2021
Page 4 Overview of the College
Page 5 Overview of Bold & Blue
Pages 6, 7 Announcing the First Endowed Professorship in the College of Natural Sciences
Page 8 Spooky Science, Astronomy Outreach, SDSU Chemistry Research Features on Journal Cover
Page 9 Students Win Business Plan Competition With Aims to Improve Shelf Life of Produce, Summer Researchers
Page 10 NIH Grant Helps Unravel Rare Inflammatory Genetic Disorders, International Excellence in South Dakota
Page 11 The Next Frontier of Science Education: Virtual Reality, SDSU Researchers Uncover how Cancer …

Mite Diet Sequences Obtained By High Throughput Sequencing Of Gut Contents Of Freshly Collected Water Mites, Adrian Amelio Vasquez, Obadeh Mohiddin, Zeyu Li, Brittany L. Bonnici, Katherine Gurdziel, Jeffrey L. Ram

Physiology Faculty Research Publications

Cytochrome oxidase subunit I (COI) barcode sequences in this file were obtained from gut DNA extracted from 54 freshly collected water mites, comprising 21 Lebertia quinquemaculosa , 30 Lebertia davidcooki , 1 Limnesia , and 2 Arrenurus specimens. Methods and other details about these sequences are described in a paper by the same authors in a submitted publication (2021: URL to be given here when published). Data on collection locations, primers (mLep and LCOI), amino acid translations, etc. are included in corresponding sequences uploaded to GenBank. The right column below contains additional notes on naming the taxa of the sequences …

Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė

Biological Sciences Faculty Publications

Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆R_rs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …

Modeling Stromatolite Formation With Diffusion-Limited Aggregation, Laura E. Stevens

Graduate Student Theses, Dissertations, & Professional Papers

Stromatolites, microbialites, and other microbially induced sedimentary structures exist in the rock record as far back as 3.6 billion years ago and continue to form in the present day. Better characterizing these structures and better understanding how they form is crucial in distinguishing these biosignatures from similar, abiotic structures, which can help us to understand the conditions of early Earth and early Mars. To that end, I have modified DLA 3D EXT, an open-source stromatolite modeling program, to more closely reflect the process of microbial trapping-and-binding by filamentous microbes in a calcite-precipitating hot spring system. This modified program includes a …

Comparing Capabilities Of Shewanella Oneidensis Mr-1 And The Microbial Community Of Iron Caves To Reduce Fe(Iii), Aaron Douglas Pham

Williams Honors College, Honors Research Projects

Caves are generally formed by the erosion and/or dissolution of rock and its subsequent removal by water. Iron ore caves (IOCs) form despite being hosted by relatively insoluble and weathering-resistant rock. Due to the discovery of a microbial community behind the walls of these caves, it was hypothesized that these bacteria could be responsible for speleogenesis. Iron ore exists in an oxidized (Fe(III)) state, but reduced (Fe(II)) form is soluble. It was further reasoned that the bacteria might be able to reduce Fe(III) through direct metabolic activity, which uses iron as an electron acceptor. Here we show that cave microorganisms …

Utilization Of Paenibacillus Polymyxa In The Recovery Of Lithium Bearing Minerals, Diana Bullen

Dissertations, Master's Theses and Master's Reports

In the global transition to green energy in the transportation and power production sectors, lithium has emerged as a viable solution, and crucial component, for the effective storage of renewable resources. To avoid further degradation of the land due to mining for virgin material, methods focused on recovering lithium must be developed. This research project seeks to explore a new way to recover lithium by using the bacterium Paenibacillus polymyxa. The bacteria were grown and then applied to the lithium bearing mineral spodumene. Settling velocity profiles were constructed for different treatments of spodumene. It was found that the spodumene …

A Snapshot Of Ancient Microbial Life: Microorganisms And Organic Compounds In Primary Fluid Inclusions In Bedded Halite, Neoproterozoic Browne Formation Of Central Australia, Sara I. Schreder-Gomes

Graduate Theses, Dissertations, and Problem Reports (ETD)

Modern shallow brine environments contain an abundance of microorganisms. Microorganisms, mineral crystals, and air bubbles can be trapped with those brines in primary fluid inclusions in bedded halite as it grows in shallow saline surface waters. Primary fluid inclusions and their contents can be preserved, unaltered, for millions of years.

The ~830 million-year-old Browne Formation of central Australia contains intervals of bedded halite with unaltered primary fluid inclusions. Intervals of bedded halite were sampled in the Empress 1A core from ~1480 m – 1520 m depths. Here, I used petrography to describe suspect microorganisms and organic compounds that were trapped …

Applied Molecular Dynamics: From Targeting Viral Helicases, To Understanding The Interactions Of Cucurbituril Complexes In Ionic Solutions, Bryan Raubenolt

LSU New Orleans Theses and Dissertations

Molecular Dynamics simulations are a highly useful tool in helping understand the fundamental interactions present in a variety of chemical systems. The work discussed here illustrates it’s use in determining the conformational dynamics of the Zika and SARS-Cov-2 helicase in a physiological environment, largely in an effort to discover inhibitors capable of rendering the protein inert. Additionally, we show how it can be used to understand paradoxical trends in the anion-induced precipitation of Cucurbituril cavitands.

Viral helicases are motor proteins tasked with unwinding the viral dsRNA, a crucial step in preparing the strand to be translatable by host cells. By …

In The Margins: Reconsidering The Range And Contribution Of Diazotrophs In Nearshore Environments, Corday R. Selden

OES Theses and Dissertations

Dinitrogen (N₂) fixation enables primary production and, consequently, carbon dioxide drawdown in nitrogen (N) limited marine systems, exerting a powerful influence over the coupled carbon and N cycles. Our understanding of the environmental factors regulating its distribution and magnitude are largely based on the range and sensitivity of one genus, Trichodesmium. However, recent work suggests that the niche preferences of distinct diazotrophic (N₂ fixing) clades differ due to their metabolic and ecological diversity, hampering efforts to close the N budget and model N₂ fixation accurately. Here, I explore the range of N₂ fixation …

Structural Characterization Of Two Large Icosahedral Dna Viruses And Their Capsid Assembly Mechanisms, Yuejiao Xian

Open Access Theses & Dissertations

In the last three decades, many large DNA viruses were discovered and grouped into a loosely defined clade of Nucleocytoplasmic Large DNA Viruses (NCLDVs). NCLDVs infect a wide range of hosts from single cellular protists to large animals. Recently, these viruses were classified as a new phylum of Nucleocytoviricota under the kingdom of Bamfordvirae. The genomes of these Nucleocytoviricota viruses (NCVs) are remarkedly large and complicated, containing many cellular genes from all three domains of life, which raised intensive debates on their evolutionary origins. Despite being classified in the same phylum, their physical structures vary and can be roughly classified …

Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The aim of this work was to evaluate the transformation of manganese oxide (hausmannite) by microscopic filamentous fungus Aspergillus niger and the effects of the transformation on mobility and bioavailability of arsenic. Our results showed that the A. niger strain CBS 140837 greatly affected the stability of hausmannite and induced its transformation into biogenic crystals of manganese oxalates—falottaite and lindbergite. The transformation was enabled by fungal acidolysis of hausmannite and subsequent release of manganese ions into the culture medium. While almost 45% of manganese was bioextracted, the arsenic content in manganese precipitates increased throughout the 25-day static cultivation of fungus. …

Potential Virus-Mediated Nitrogen Cycling In Oxygen-Depleted Oceanic Waters, M. Consuelo Gazitúa, Dean R. Vik, Simon Roux, Ann C. Gregory, Benjamin Bolduc, Brittany Widner, Margaret R. Mulholland, Steven J. Hallam, Osvaldo Ulloa, Matthew B. Sullivan

OES Faculty Publications

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ …

Graphene-Based Electrochemical Aptasensor For The Detection Of Salmonella Typhimurium, Shalini Muniandy

Student Works (2020-2029)

Recent foodborne outbreaks in multiple locations necessitate the continuous development of highly sensitive and specific biosensors that offer rapid and sensitive detection of foodborne pathogens. The emergence of electrochemical aptasensor which is a compact analytical device with a combination of an aptamer as the biorecognition element integrated on the transducer surface created a breakthrough in the detection of foodborne bacterial pathogens. Graphene has emerged as a promising nanomaterial for reliable detection of pathogenic bacteria due to its exceptional properties such as high electrical conductivity, large surface to volume ratio, high mechanical strength and its unique interactions with DNA bases of …

Small Molecule Synthetic Carbohydrate Receptors, Marcelo F. Bravo Carranco

Dissertations, Theses, and Capstone Projects

Carbohydrate – receptor interactions are often involved in the attachment of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered “undruggable”, meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs) – small molecules that bind carbohydrates – could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of …

1,4-Dioxane Biodegradation In Propanotrophs: Molecular Foundations And Implications For Environmental Remediation, Li Fei

Dissertations

1,4-Dioxane (dioxane) has emerged with an escalating concern given its human carcinogenicity and widespread occurrence in groundwater. Bioremediation is promising as an effective and cost-efficient treatment alternative for in situ or ex situ cleanup of dioxane and co-existing pollutants in the field. Soluble di-iron monooxygenases (SDIMOs) are reputed for their essential roles in initiating the cleavage of dioxane and other pollutants. In this doctoral dissertation, molecular foundations for SDIMOs-mediated dioxane biodegradation are untangled to promote the development and implication of site-specific bioremediation and natural attenuation strategies. This dissertation focused on propanotrophic bacteria given their pivotal roles in dioxane metabolism and …

Innovative Approaches In The Discovery Of Aquatic Mycobacteriophages, Janis H. Doss

Biomedical Sciences Theses & Dissertations

Bacteriophages (phages), viruses that infect bacteria, have many applications in medicine, agriculture, molecular biology, and other fields. As antibiotic resistance becomes an increasing problem, interest in phages has grown. The traditional techniques of phage discovery are successful for some phages, but others require modified procedures to achieve detectable host infection.

Mycobacterium is a diverse bacterial genus characterized by a unique cell wall containing mycolic acids, which aids in survival and pathogenesis. The aims of the present research were to isolate mycobacteriophages, use bioinformatics techniques to analyze mycobacterial prophages, and combine genetic analysis with multi-well plate host range studies to identify …